I don't think anything was wrong with your MBR or your drive when the newly created partitions showed up as raw. I'm afraid I don't know why it sometimes can't be selected by the drop down menu in gparted. Some background may help you understand what should be happening, however.
First: the MBR. For an external drive the MBR is only a container for the primary partition table. That table takes up most of the last 64 bytes of the MBR, which is itself the first 512 bytes of data on the drive.
For a bootable drive the MBR contains code to load the beginning of grub, or to load the beginning of the first bootable partition (e.g. Windows or DOS). The latter is usually pretty interchangeable and you can use the Windows utilities to replace a vanilla one for that matter. If the drive needs something special there, however, it could use a special manufacturer provided MBR. For recent drives that's probably pretty unusual.
When you used gparted you specified a type for each partition. You should make sure that those are correct.
The partitions are raw until you create file systems on them. They can be Ext 3, for Unix, or NTFS or a version of FAT for Windows. For Ubuntu this is usually done by the Ubuntu installer. gparted wrote a new primary partition table at the end of the external disks MBR, and maybe wrote some other partition information elsewhere if you defined any external partitions. The Ubuntu installer will fill the partitions you tell it to with the file systems you tell it to create, wiping out any data there. Then they will no longer be raw (though the swap one will be).
When installing Ubuntu the system will also want to install GRUB2 to produce a boot window to select what system to boot. By default this goes on the primary disk (the one the system boots from). This changes the code in the first part of the MBR on that drive and installs Grub2 on some (usually) free space between the MBR and the end of the first track. (The MBR is the first sector of the first track of a drive).
Grub could also be installed on the MBR on secondary disk if you can tell your BIOS to boot from there.
It can also be installed into partitions on the secondary disk. If you do that you need to be sure the code in the MBR is good, the one installed by Windows would work fine. The partition with Grub installed would have to be marked as the bootable one.
When you are booting Windows, Grub finds the partition it is on and then loads the first sector of its partition, just like the original MBR did. When booting a Linux kernel Grub actually loads the whole kernel and starts it up.
Since the primary partition table takes up most of the last 64 of the last 66 bytes of the MBR you can't simply use a sector copy to replace it without wiping out your partition table. If you've done that, however, you should be able to use gparted to recreate it. gparted shouldn't wipe out the code part of the MBR in any case.